Settings defining the calculation of fitness. More...

Inheritance diagram for denoptim.fitness.FitnessParameters:

Collaboration diagram for denoptim.fitness.FitnessParameters:

Public Member Functions
	FitnessParameters ()
	Constructor. More...

boolean	useExternalFitness ()

boolean	makePictures ()

boolean	make3dTree ()

boolean	checkPreFitnessUID ()

String	getExternalFitnessProvider ()
	Gets the pathname of the external executable file. More...

String	getExternalFitnessProviderInterpreter ()
	Gets the interpreter used to run the external fitness provider. More...

String	getFitnessExpression ()

List< DescriptorForFitness >	getDescriptors ()

void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

boolean	writeCandidatesOnDisk ()

Public Member Functions inherited from denoptim.programs.RunTimeParameters
	RunTimeParameters (ParametersType paramType)
	Constructor. More...

String	paramTypeName ()
	Returns a string defining the type the parameters collected here. More...

String	getWorkDirectory ()
	Gets the pathname to the working directory. More...

void	setWorkDirectory (String pathname)
	Gets the pathname to the working directory. More...

String	getLogFilePathname ()
	Gets the pathname to the log file. More...

void	setLogFilePathname (String pathname)
	Sets the pathname to the log file. More...

Logger	getLogger ()
	Get the name of the program specific logger. More...

Logger	startProgramSpecificLogger (String loggerIdentifier) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startProgramSpecificLogger (String loggerIdentifier, boolean toLogFile) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startConsoleLogger (String loggerIdentifier)
	Starts a program-specific logger that prints to System.err stream. More...

int	getVerbosity ()
	Returns the level of verbosity, i.e., the amount of log that we want to print. More...

void	setVerbosity (int l)
	Set the level of verbosity. More...

Randomizer	getRandomizer ()
	Returns the current program-specific randomizer. More...

long	getRandomSeed ()
	Returns the seed. More...

void	setRandomizer (Randomizer rng)
	Sets the randomizer. More...

Randomizer	startRandomizer ()
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

Randomizer	startRandomizer (long seed)
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

void	readParameterFile (String infile) throws DENOPTIMException
	Read the parameter TXT file line by line and interpret its content. More...

void	readParameterLine (String line) throws DENOPTIMException

boolean	containsParameters (ParametersType type)

RunTimeParameters	getParameters (ParametersType type)

void	setParameters (RunTimeParameters otherParams)

void	interpretKeyword (String line) throws DENOPTIMException
	Processes a string looking for keyword and a possibly associated value. More...

abstract void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

abstract void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

abstract void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

abstract String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

void	printParameters ()
	Print all parameters. More...

Private Attributes
boolean	useExternalFitness = true
	Flag indication we want to use external fitness provider. More...

String	externalExe = ""
	Pathname of an external fitness provider executable. More...

String	interpreterExternalExe = "bash"
	Interpreter for the external fitness provider. More...

String	fitnessExpression = ""
	Formulation of the internally provided fitness. More...

List< String >	customVarDescExpressions
	List of custom variable definitions read from input. More...

List< DescriptorForFitness >	descriptors
	The list of descriptors needed to calculate the variables that are used to calculate the fitness with the internal fitness provider. More...

boolean	makePictures = false
	Flag controlling production of png graphics for each candidate. More...

boolean	make3DTrees = true
	Flag requesting the generation of a 3d-tree model instead of a plain collection of 3d building blocks. More...

boolean	checkPreFitnessUID = true
	Flag requesting to test for uniqueness of a candidate based on the unique identifier (UID) generated by conversion of the graph into a molecular entity. More...

boolean	checkPreFitnessUIDFromInput = false
	Flag recording that we have explicitly expressed the choice of checkPreFitnessUID. More...

boolean	writeCandidatesOnDisk = true
	Flag requesting to write a file that collects all info on an evaluated candidate, i.e., the "FIT" file, even in case of internal fitness. More...

Additional Inherited Members
Static Public Member Functions inherited from denoptim.programs.RunTimeParameters
static boolean	readYesNoTrueFalse (String s)
	Reads a string searching for any common way to say either yes/true (including shorthand t/y) or no/false (including shorthand f/n either). More...

Public Attributes inherited from denoptim.programs.RunTimeParameters
final String	NL = System.getProperty("line.separator")
	New line character. More...

Protected Member Functions inherited from denoptim.programs.RunTimeParameters
void	checkOtherParameters () throws DENOPTIMException
	Checks any of the parameter collections contained in this instance. More...

void	processOtherParameters () throws DENOPTIMException
	Processes any of the parameter collections contained in this instance. More...

void	ensureFileExistsIfSet (String pathname)
	Ensures a pathname is not empty nor null and that it does lead to an existing file or triggers an error. More...

void	ensureFileExists (String pathname)
	Ensures a pathname does lead to an existing file or triggers an error. More...

void	ensureNotNull (String paramName, String param, String paramKey)
	Ensures that a parameter is not null or triggers an error. More...

void	ensureIsPositive (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureIsPositiveOrZero (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureInRange (String paramName, int value, int min, int max, String paramKey)
	Ensures that a parameter is within a range or triggers an error. More...

Protected Attributes inherited from denoptim.programs.RunTimeParameters
boolean	isMaster = true
	Flag signaling this is the master collection of parameters. More...

String	workDir = System.getProperty("user.dir")
	Working directory. More...

String	logFile = "unset"
	Log file. More...

int	verbosity = 0
	Verbosity level for logger. More...

Map< ParametersType, RunTimeParameters >	otherParameters
	Collection of other parameters by type. More...

Detailed Description

Settings defining the calculation of fitness.

Author: Marco Foscato

Definition at line 35 of file FitnessParameters.java.

Constructor & Destructor Documentation

◆ FitnessParameters()

denoptim.fitness.FitnessParameters.FitnessParameters ( )

Constructor.

Definition at line 115 of file FitnessParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.FIT_PARAMS.

Member Function Documentation

◆ checkParameters()

void denoptim.fitness.FitnessParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 259 of file FitnessParameters.java.

References denoptim.files.FileUtils.checkExists(), denoptim.programs.RunTimeParameters.checkOtherParameters(), and denoptim.fitness.FitnessParameters.externalExe.

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◆ checkPreFitnessUID()

boolean denoptim.fitness.FitnessParameters.checkPreFitnessUID ( )

Returns: true if we want to check the unique identifier (UID) of candidates prior to submitting them to the fitness provider.

Definition at line 161 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.checkPreFitnessUID.

◆ getDescriptors()

List< DescriptorForFitness > denoptim.fitness.FitnessParameters.getDescriptors ( )

Returns: list of descriptors needed to calculate the fitness

Definition at line 204 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.descriptors.

Referenced by denoptim.task.FitnessTask.runInternalFitness(), denoptim.fitness.FitnessProviderTest.testGetConstantFitness(), denoptim.fitness.FitnessProviderTest.testGetFitnessWithParametrizedDescriptors(), and denoptim.fitness.FitnessExpressionParserTest.testProcessExpressions().

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◆ getExternalFitnessProvider()

String denoptim.fitness.FitnessParameters.getExternalFitnessProvider ( )

Gets the pathname of the external executable file.

Returns: the pathname to the external fitness provider.

Definition at line 172 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.externalExe.

Referenced by denoptim.task.FitnessTask.runExternalFitness().

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◆ getExternalFitnessProviderInterpreter()

String denoptim.fitness.FitnessParameters.getExternalFitnessProviderInterpreter ( )

Gets the interpreter used to run the external fitness provider.

Returns: the interpreter name.

Definition at line 183 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.interpreterExternalExe.

Referenced by denoptim.task.FitnessTask.runExternalFitness().

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◆ getFitnessExpression()

String denoptim.fitness.FitnessParameters.getFitnessExpression ( )

Returns: the expression used to calculate the fitness with the internal fitness provider

Definition at line 194 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.fitnessExpression.

Referenced by denoptim.task.FitnessTask.runInternalFitness(), denoptim.fitness.FitnessProviderTest.testGetConstantFitness(), and denoptim.fitness.FitnessProviderTest.testGetFitnessWithParametrizedDescriptors().

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◆ getPrintedList()

String denoptim.fitness.FitnessParameters.getPrintedList ( )

Returns the list of parameters in a string with newline characters as delimiters.

Returns: the list of parameters in a string with newline characters as delimiters.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 295 of file FitnessParameters.java.

References denoptim.programs.RunTimeParameters.NL, denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.paramTypeName().

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◆ interpretKeyword()

void denoptim.fitness.FitnessParameters.interpretKeyword	(	String	key,
		String	value
	)		throws DENOPTIMException

Processes a keyword/value pair and assign the related parameters.

Parameters

key	the keyword as string
value	the value as a string

Exceptions

DENOPTIMException is the parameter cannot be configured from the given value.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 211 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessProviderTest.testGetConstantFitness(), denoptim.fitness.FitnessProviderTest.testGetFitnessWithParametrizedDescriptors(), and denoptim.fitness.FitnessExpressionParserTest.testProcessExpressions().

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◆ make3dTree()

boolean denoptim.fitness.FitnessParameters.make3dTree ( )

Returns: true if we are asked to make a tree-like 3d molecular model prior fitness evaluation. The model is built by aligning 3d-building blocks to the attachment point vectors, so there is no energy refinement.

Definition at line 150 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.make3DTrees.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), and denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call().

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◆ makePictures()

boolean denoptim.fitness.FitnessParameters.makePictures ( )

Returns: true if generation of the candidate's picture is required.

Definition at line 137 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.makePictures.

◆ processParameters()

void denoptim.fitness.FitnessParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 273 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessProviderTest.testGetConstantFitness(), denoptim.fitness.FitnessProviderTest.testGetFitnessWithParametrizedDescriptors(), and denoptim.fitness.FitnessExpressionParserTest.testProcessExpressions().

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◆ useExternalFitness()

boolean denoptim.fitness.FitnessParameters.useExternalFitness ( )

Returns: true if we are asked to execute an external fitness provider.

Definition at line 126 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.useExternalFitness.

◆ writeCandidatesOnDisk()

boolean denoptim.fitness.FitnessParameters.writeCandidatesOnDisk ( )

Returns: true if we are asked to write on disk every candidate that has been evaluated.

Definition at line 326 of file FitnessParameters.java.

References denoptim.fitness.FitnessParameters.writeCandidatesOnDisk.

Member Data Documentation

◆ checkPreFitnessUID

boolean denoptim.fitness.FitnessParameters.checkPreFitnessUID = true

private

Flag requesting to test for uniqueness of a candidate based on the unique identifier (UID) generated by conversion of the graph into a molecular entity.

Definition at line 92 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.checkPreFitnessUID(), denoptim.fitness.FitnessParameters.interpretKeyword(), and denoptim.fitness.FitnessParameters.processParameters().

◆ checkPreFitnessUIDFromInput

boolean denoptim.fitness.FitnessParameters.checkPreFitnessUIDFromInput = false

private

Flag recording that we have explicitly expressed the choice of checkPreFitnessUID.

Definition at line 98 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.interpretKeyword(), and denoptim.fitness.FitnessParameters.processParameters().

◆ customVarDescExpressions

List<String> denoptim.fitness.FitnessParameters.customVarDescExpressions

private

Initial value:

=

new ArrayList<String>()

List of custom variable definitions read from input.

These lines are the definition of atom/bond specific descriptors, and custom parametrised descriptors.

Definition at line 62 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.interpretKeyword(), and denoptim.fitness.FitnessParameters.processParameters().

◆ descriptors

List<DescriptorForFitness> denoptim.fitness.FitnessParameters.descriptors

private

Initial value:

=

new ArrayList<DescriptorForFitness>()

The list of descriptors needed to calculate the variables that are used to calculate the fitness with the internal fitness provider.

Definition at line 69 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.getDescriptors(), and denoptim.fitness.FitnessParameters.processParameters().

◆ externalExe

String denoptim.fitness.FitnessParameters.externalExe = ""

private

Pathname of an external fitness provider executable.

Definition at line 45 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.checkParameters(), denoptim.fitness.FitnessParameters.getExternalFitnessProvider(), and denoptim.fitness.FitnessParameters.interpretKeyword().

◆ fitnessExpression

String denoptim.fitness.FitnessParameters.fitnessExpression = ""

private

Formulation of the internally provided fitness.

Definition at line 55 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.getFitnessExpression(), denoptim.fitness.FitnessParameters.interpretKeyword(), and denoptim.fitness.FitnessParameters.processParameters().

◆ interpreterExternalExe

String denoptim.fitness.FitnessParameters.interpreterExternalExe = "bash"

private

Interpreter for the external fitness provider.

Definition at line 50 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.getExternalFitnessProviderInterpreter(), and denoptim.fitness.FitnessParameters.interpretKeyword().

◆ make3DTrees

boolean denoptim.fitness.FitnessParameters.make3DTrees = true

private

Flag requesting the generation of a 3d-tree model instead of a plain collection of 3d building blocks.

In the latter, the coordinated of each fragment are not changed when building the molecular representation that is sent to the fitness provider. Setting this to true asks for roto-translation of each fragment, but does not perform any energy-driven refinement of the geometry.

Definition at line 85 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.interpretKeyword(), and denoptim.fitness.FitnessParameters.make3dTree().

◆ makePictures

boolean denoptim.fitness.FitnessParameters.makePictures = false

private

Flag controlling production of png graphics for each candidate.

Definition at line 75 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.interpretKeyword(), denoptim.fitness.FitnessParameters.makePictures(), and denoptim.task.FitnessTask.runFitnessProvider().

◆ useExternalFitness

boolean denoptim.fitness.FitnessParameters.useExternalFitness = true

private

Flag indication we want to use external fitness provider.

Definition at line 40 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.interpretKeyword(), denoptim.fitness.FitnessParameters.processParameters(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.fitness.FitnessParameters.useExternalFitness().

◆ writeCandidatesOnDisk

boolean denoptim.fitness.FitnessParameters.writeCandidatesOnDisk = true

private

Flag requesting to write a file that collects all info on an evaluated candidate, i.e., the "FIT" file, even in case of internal fitness.

When this is true, we write one file for each evaluated candidate. Note that in case of external fitness provider this file is created by the external fitness provider and this flag has no effect.

Definition at line 107 of file FitnessParameters.java.

Referenced by denoptim.fitness.FitnessParameters.interpretKeyword(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.fitness.FitnessParameters.writeCandidatesOnDisk().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/fitness/FitnessParameters.java

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FitnessParameters()

Member Function Documentation

◆ checkParameters()

◆ checkPreFitnessUID()

◆ getDescriptors()

◆ getExternalFitnessProvider()

◆ getExternalFitnessProviderInterpreter()

◆ getFitnessExpression()

◆ getPrintedList()

◆ interpretKeyword()

◆ make3dTree()

◆ makePictures()

◆ processParameters()

◆ useExternalFitness()

◆ writeCandidatesOnDisk()

Member Data Documentation

◆ checkPreFitnessUID

◆ checkPreFitnessUIDFromInput

◆ customVarDescExpressions

◆ descriptors

◆ externalExe

◆ fitnessExpression

◆ interpreterExternalExe

◆ make3DTrees

◆ makePictures

◆ useExternalFitness

◆ writeCandidatesOnDisk